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45 #include "gromacs/gmxlib/network.h"
46 #include "gromacs/linearalgebra/nrjac.h"
47 #include "gromacs/math/do_fit.h"
48 #include "gromacs/math/functions.h"
49 #include "gromacs/math/vec.h"
50 #include "gromacs/mdrunutility/multisim.h"
51 #include "gromacs/mdtypes/commrec.h"
52 #include "gromacs/mdtypes/fcdata.h"
53 #include "gromacs/mdtypes/inputrec.h"
54 #include "gromacs/mdtypes/mdatom.h"
55 #include "gromacs/mdtypes/state.h"
56 #include "gromacs/pbcutil/ishift.h"
57 #include "gromacs/pbcutil/pbc.h"
58 #include "gromacs/topology/ifunc.h"
59 #include "gromacs/topology/mtop_util.h"
60 #include "gromacs/topology/topology.h"
61 #include "gromacs/utility/arrayref.h"
62 #include "gromacs/utility/fatalerror.h"
63 #include "gromacs/utility/pleasecite.h"
64 #include "gromacs/utility/smalloc.h"
69 // TODO This implementation of ensemble orientation restraints is nasty because
70 // a user can't just do multi-sim with single-sim orientation restraints.
72 void init_orires(FILE* fplog,
73 const gmx_mtop_t& mtop,
76 const gmx_multisim_t* ms,
80 od->nr = gmx_mtop_ftype_count(mtop, F_ORIRES);
83 /* Not doing orientation restraints */
87 const int numFitParams = 5;
88 if (od->nr <= numFitParams)
91 "The system has %d orientation restraints, but at least %d are required, since "
92 "there are %d fitting parameters.",
98 if (ir->bPeriodicMols)
100 /* Since we apply fitting, we need to make molecules whole and this
101 * can not be done when periodic molecules are present.
104 "Orientation restraints can not be applied when periodic molecules are present "
111 "Orientation restraints do not work with MPI parallelization. Choose 1 MPI rank, "
115 GMX_RELEASE_ASSERT(globalState != nullptr, "We need a valid global state in init_orires");
117 od->fc = ir->orires_fc;
124 int* nr_ex = nullptr;
125 int typeMin = INT_MAX;
127 for (const auto il : IListRange(mtop))
129 const int numOrires = il.list()[F_ORIRES].size();
130 if (il.nmol() > 1 && numOrires > 0)
133 "Found %d copies of a molecule with orientation restrains while the current "
134 "code only supports a single copy. If you want to ensemble average, run "
135 "multiple copies of the system using the multi-sim feature of mdrun.",
139 for (int i = 0; i < numOrires; i += 3)
141 int type = il.list()[F_ORIRES].iatoms[i];
142 int ex = mtop.ffparams.iparams[type].orires.ex;
145 srenew(nr_ex, ex + 1);
146 for (int j = od->nex; j < ex + 1; j++)
152 GMX_ASSERT(nr_ex, "Check for allocated nr_ex to keep the static analyzer happy");
155 typeMin = std::min(typeMin, type);
156 typeMax = std::max(typeMax, type);
159 /* With domain decomposition we use the type index for indexing in global arrays */
161 typeMax - typeMin + 1 == od->nr,
162 "All orientation restraint parameter entries in the topology should be consecutive");
163 /* Store typeMin so we can index array with the type offset */
164 od->typeMin = typeMin;
166 snew(od->S, od->nex);
167 /* When not doing time averaging, the instaneous and time averaged data
168 * are indentical and the pointers can point to the same memory.
170 snew(od->Dinsl, od->nr);
174 snew(od->Dins, od->nr);
178 od->Dins = od->Dinsl;
181 if (ir->orires_tau == 0)
189 snew(od->Dtav, od->nr);
190 od->edt = std::exp(-ir->delta_t / ir->orires_tau);
191 od->edt_1 = 1.0 - od->edt;
193 /* Extend the state with the orires history */
194 globalState->flags |= enumValueToBitMask(StateEntry::OrireInitF);
195 globalState->hist.orire_initf = 1;
196 globalState->flags |= enumValueToBitMask(StateEntry::OrireDtav);
197 globalState->hist.norire_Dtav = od->nr * 5;
198 snew(globalState->hist.orire_Dtav, globalState->hist.norire_Dtav);
201 snew(od->oinsl, od->nr);
204 snew(od->oins, od->nr);
208 od->oins = od->oinsl;
210 if (ir->orires_tau == 0)
216 snew(od->otav, od->nr);
218 snew(od->tmpEq, od->nex);
221 for (int i = 0; i < mtop.natoms; i++)
223 if (getGroupType(mtop.groups, SimulationAtomGroupType::OrientationRestraintsFit, i) == 0)
228 snew(od->mref, od->nref);
229 snew(od->xref, od->nref);
230 snew(od->xtmp, od->nref);
232 snew(od->eig, od->nex * 12);
234 /* Determine the reference structure on the master node.
235 * Copy it to the other nodes after checking multi compatibility,
236 * so we are sure the subsystems match before copying.
238 auto x = makeArrayRef(globalState->x);
239 rvec com = { 0, 0, 0 };
242 for (const AtomProxy atomP : AtomRange(mtop))
244 const t_atom& local = atomP.atom();
245 int i = atomP.globalAtomNumber();
246 if (mtop.groups.groupNumbers[SimulationAtomGroupType::OrientationRestraintsFit].empty()
247 || mtop.groups.groupNumbers[SimulationAtomGroupType::OrientationRestraintsFit][i] == 0)
249 /* Not correct for free-energy with changing masses */
250 od->mref[j] = local.m;
251 // Note that only one rank per sim is supported.
254 copy_rvec(x[i], od->xref[j]);
255 for (int d = 0; d < DIM; d++)
257 com[d] += od->mref[j] * x[i][d];
264 svmul(1.0 / mtot, com, com);
267 for (int j = 0; j < od->nref; j++)
269 rvec_dec(od->xref[j], com);
273 fprintf(fplog, "Found %d orientation experiments\n", od->nex);
274 for (int i = 0; i < od->nex; i++)
276 fprintf(fplog, " experiment %d has %d restraints\n", i + 1, nr_ex[i]);
281 fprintf(fplog, " the fit group consists of %d atoms and has total mass %g\n", od->nref, mtot);
285 fprintf(fplog, " the orientation restraints are ensemble averaged over %d systems\n", ms->numSimulations_);
287 check_multi_int(fplog, ms, od->nr, "the number of orientation restraints", FALSE);
288 check_multi_int(fplog, ms, od->nref, "the number of fit atoms for orientation restraining", FALSE);
289 check_multi_int(fplog, ms, ir->nsteps, "nsteps", FALSE);
290 /* Copy the reference coordinates from the master to the other nodes */
291 gmx_sum_sim(DIM * od->nref, od->xref[0], ms);
294 please_cite(fplog, "Hess2003");
297 void diagonalize_orires_tensors(t_oriresdata* od)
299 if (od->M == nullptr)
302 for (int i = 0; i < DIM; i++)
306 snew(od->eig_diag, DIM);
308 for (int i = 0; i < DIM; i++)
314 for (int ex = 0; ex < od->nex; ex++)
316 /* Rotate the S tensor back to the reference frame */
318 mmul(od->R, od->S[ex], TMP);
319 mtmul(TMP, od->R, S);
320 for (int i = 0; i < DIM; i++)
322 for (int j = 0; j < DIM; j++)
324 od->M[i][j] = S[i][j];
329 jacobi(od->M, DIM, od->eig_diag, od->v, &nrot);
332 for (int i = 0; i < DIM; i++)
336 for (int i = 0; i < DIM; i++)
338 for (int j = i + 1; j < DIM; j++)
340 if (gmx::square(od->eig_diag[ord[j]]) > gmx::square(od->eig_diag[ord[i]]))
349 for (int i = 0; i < DIM; i++)
351 od->eig[ex * 12 + i] = od->eig_diag[ord[i]];
353 for (int i = 0; i < DIM; i++)
355 for (int j = 0; j < DIM; j++)
357 od->eig[ex * 12 + 3 + 3 * i + j] = od->v[j][ord[i]];
363 void print_orires_log(FILE* log, t_oriresdata* od)
367 diagonalize_orires_tensors(od);
369 for (int ex = 0; ex < od->nex; ex++)
371 eig = od->eig + ex * 12;
372 fprintf(log, " Orientation experiment %d:\n", ex + 1);
373 fprintf(log, " order parameter: %g\n", eig[0]);
374 for (int i = 0; i < DIM; i++)
377 " eig: %6.3f %6.3f %6.3f %6.3f\n",
378 (eig[0] != 0) ? eig[i] / eig[0] : eig[i],
379 eig[DIM + i * DIM + XX],
380 eig[DIM + i * DIM + YY],
381 eig[DIM + i * DIM + ZZ]);
387 real calc_orires_dev(const gmx_multisim_t* ms,
389 const t_iatom forceatoms[],
390 const t_iparams ip[],
392 ArrayRef<const RVec> xWholeMolecules,
396 const history_t* hist)
399 real edt, edt_1, invn, pfac, r2, invr, corrfac, wsv2, sw, dev;
403 rvec * xref, *xtmp, com, r_unrot, r;
405 const real two_thr = 2.0 / 3.0;
409 /* This means that this is not the master node */
411 "Orientation restraints are only supported on the master rank, use fewer ranks");
414 bTAV = (od->edt != 0);
425 od->exp_min_t_tau = hist->orire_initf * edt;
427 /* Correction factor to correct for the lack of history
430 corrfac = 1.0 / (1.0 - od->exp_min_t_tau);
439 invn = 1.0 / ms->numSimulations_;
449 auto massT = md->massT;
450 auto cORF = md->cORF;
451 for (int i = 0; i < md->nr; i++)
455 copy_rvec(xWholeMolecules[i], xtmp[j]);
457 for (int d = 0; d < DIM; d++)
459 com[d] += mref[j] * xtmp[j][d];
465 svmul(1.0 / mtot, com, com);
466 for (int j = 0; j < nref; j++)
468 rvec_dec(xtmp[j], com);
470 /* Calculate the rotation matrix to rotate x to the reference orientation */
471 calc_fit_R(DIM, nref, mref, xref, xtmp, od->R);
473 for (int fa = 0; fa < nfa; fa += 3)
475 const int type = forceatoms[fa];
476 const int restraintIndex = type - od->typeMin;
479 pbc_dx_aiuc(pbc, x[forceatoms[fa + 1]], x[forceatoms[fa + 2]], r_unrot);
483 rvec_sub(x[forceatoms[fa + 1]], x[forceatoms[fa + 2]], r_unrot);
485 mvmul(od->R, r_unrot, r);
487 invr = gmx::invsqrt(r2);
488 /* Calculate the prefactor for the D tensor, this includes the factor 3! */
489 pfac = ip[type].orires.c * invr * invr * 3;
490 for (int i = 0; i < ip[type].orires.power; i++)
494 rvec5& Dinsl = od->Dinsl[restraintIndex];
495 Dinsl[0] = pfac * (2 * r[0] * r[0] + r[1] * r[1] - r2);
496 Dinsl[1] = pfac * (2 * r[0] * r[1]);
497 Dinsl[2] = pfac * (2 * r[0] * r[2]);
498 Dinsl[3] = pfac * (2 * r[1] * r[1] + r[0] * r[0] - r2);
499 Dinsl[4] = pfac * (2 * r[1] * r[2]);
503 for (int i = 0; i < 5; i++)
505 od->Dins[restraintIndex][i] = Dinsl[i] * invn;
512 gmx_sum_sim(5 * od->nr, od->Dins[0], ms);
515 /* Calculate the order tensor S for each experiment via optimization */
516 for (int ex = 0; ex < od->nex; ex++)
518 for (int i = 0; i < 5; i++)
520 matEq[ex].rhs[i] = 0;
521 for (int j = 0; j <= i; j++)
523 matEq[ex].mat[i][j] = 0;
528 for (int fa = 0; fa < nfa; fa += 3)
530 const int type = forceatoms[fa];
531 const int restraintIndex = type - od->typeMin;
532 rvec5& Dtav = od->Dtav[restraintIndex];
535 /* Here we update Dtav in t_fcdata using the data in history_t.
536 * Thus the results stay correct when this routine
537 * is called multiple times.
539 for (int i = 0; i < 5; i++)
541 Dtav[i] = edt * hist->orire_Dtav[restraintIndex * 5 + i]
542 + edt_1 * od->Dins[restraintIndex][i];
546 int ex = ip[type].orires.ex;
547 real weight = ip[type].orires.kfac;
548 /* Calculate the vector rhs and half the matrix T for the 5 equations */
549 for (int i = 0; i < 5; i++)
551 matEq[ex].rhs[i] += Dtav[i] * ip[type].orires.obs * weight;
552 for (int j = 0; j <= i; j++)
554 matEq[ex].mat[i][j] += Dtav[i] * Dtav[j] * weight;
558 /* Now we have all the data we can calculate S */
559 for (int ex = 0; ex < od->nex; ex++)
561 OriresMatEq& eq = matEq[ex];
562 /* Correct corrfac and copy one half of T to the other half */
563 for (int i = 0; i < 5; i++)
565 eq.rhs[i] *= corrfac;
566 eq.mat[i][i] *= gmx::square(corrfac);
567 for (int j = 0; j < i; j++)
569 eq.mat[i][j] *= gmx::square(corrfac);
570 eq.mat[j][i] = eq.mat[i][j];
573 m_inv_gen(&eq.mat[0][0], 5, &eq.mat[0][0]);
574 /* Calculate the orientation tensor S for this experiment */
575 matrix& S = od->S[ex];
581 for (int i = 0; i < 5; i++)
583 S[0][0] += 1.5 * eq.mat[0][i] * eq.rhs[i];
584 S[0][1] += 1.5 * eq.mat[1][i] * eq.rhs[i];
585 S[0][2] += 1.5 * eq.mat[2][i] * eq.rhs[i];
586 S[1][1] += 1.5 * eq.mat[3][i] * eq.rhs[i];
587 S[1][2] += 1.5 * eq.mat[4][i] * eq.rhs[i];
592 S[2][2] = -S[0][0] - S[1][1];
595 const matrix* S = od->S;
600 for (int fa = 0; fa < nfa; fa += 3)
602 const int type = forceatoms[fa];
603 const int restraintIndex = type - od->typeMin;
604 const int ex = ip[type].orires.ex;
606 const rvec5& Dtav = od->Dtav[restraintIndex];
607 od->otav[restraintIndex] =
609 * (S[ex][0][0] * Dtav[0] + S[ex][0][1] * Dtav[1] + S[ex][0][2] * Dtav[2]
610 + S[ex][1][1] * Dtav[3] + S[ex][1][2] * Dtav[4]);
613 const rvec5& Dins = od->Dins[restraintIndex];
614 od->oins[restraintIndex] =
616 * (S[ex][0][0] * Dins[0] + S[ex][0][1] * Dins[1] + S[ex][0][2] * Dins[2]
617 + S[ex][1][1] * Dins[3] + S[ex][1][2] * Dins[4]);
621 /* When ensemble averaging is used recalculate the local orientation
622 * for output to the energy file.
624 const rvec5& Dinsl = od->Dinsl[restraintIndex];
625 od->oinsl[restraintIndex] =
627 * (S[ex][0][0] * Dinsl[0] + S[ex][0][1] * Dinsl[1] + S[ex][0][2] * Dinsl[2]
628 + S[ex][1][1] * Dinsl[3] + S[ex][1][2] * Dinsl[4]);
631 dev = od->otav[restraintIndex] - ip[type].orires.obs;
633 wsv2 += ip[type].orires.kfac * gmx::square(dev);
634 sw += ip[type].orires.kfac;
636 od->rmsdev = std::sqrt(wsv2 / sw);
638 /* Rotate the S matrices back, so we get the correct grad(tr(S D)) */
639 for (int ex = 0; ex < od->nex; ex++)
642 tmmul(od->R, od->S[ex], RS);
643 mmul(RS, od->R, od->S[ex]);
648 /* Approx. 120*nfa/3 flops */
652 const t_iatom forceatoms[],
653 const t_iparams ip[],
658 real gmx_unused lambda,
659 real gmx_unused* dvdlambda,
660 gmx::ArrayRef<const real> /*charge*/,
661 t_fcdata gmx_unused* fcd,
662 t_disresdata gmx_unused* disresdata,
663 t_oriresdata* oriresdata,
664 int gmx_unused* global_atom_index)
666 int ex, power, ki = gmx::c_centralShiftIndex;
667 real r2, invr, invr2, fc, smooth_fc, dev, devins, pfac;
674 if (oriresdata->fc != 0)
676 bTAV = (oriresdata->edt != 0);
678 smooth_fc = oriresdata->fc;
681 /* Smoothly switch on the restraining when time averaging is used */
682 smooth_fc *= (1.0 - oriresdata->exp_min_t_tau);
685 for (int fa = 0; fa < nfa; fa += 3)
687 const int type = forceatoms[fa];
688 const int ai = forceatoms[fa + 1];
689 const int aj = forceatoms[fa + 2];
690 const int restraintIndex = type - oriresdata->typeMin;
693 ki = pbc_dx_aiuc(pbc, x[ai], x[aj], r);
697 rvec_sub(x[ai], x[aj], r);
700 invr = gmx::invsqrt(r2);
702 ex = ip[type].orires.ex;
703 power = ip[type].orires.power;
704 fc = smooth_fc * ip[type].orires.kfac;
705 dev = oriresdata->otav[restraintIndex] - ip[type].orires.obs;
708 * there is no real potential when time averaging is applied
710 vtot += 0.5 * fc * gmx::square(dev);
714 /* Calculate the force as the sqrt of tav times instantaneous */
715 devins = oriresdata->oins[restraintIndex] - ip[type].orires.obs;
716 if (dev * devins <= 0)
722 dev = std::sqrt(dev * devins);
730 pfac = fc * ip[type].orires.c * invr2;
731 for (int i = 0; i < power; i++)
735 mvmul(oriresdata->S[ex], r, Sr);
736 for (int i = 0; i < DIM; i++)
738 fij[i] = -pfac * dev * (4 * Sr[i] - 2 * (2 + power) * invr2 * iprod(Sr, r) * r[i]);
741 for (int i = 0; i < DIM; i++)
747 fshift[ki][i] += fij[i];
748 fshift[gmx::c_centralShiftIndex][i] -= fij[i];
756 /* Approx. 80*nfa/3 flops */
759 void update_orires_history(const t_oriresdata& od, history_t* hist)
763 /* Copy the new time averages that have been calculated
764 * in calc_orires_dev.
766 hist->orire_initf = od.exp_min_t_tau;
767 for (int pair = 0; pair < od.nr; pair++)
769 for (int i = 0; i < 5; i++)
771 hist->orire_Dtav[pair * 5 + i] = od.Dtav[pair][i];